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nosoi: A Forward Agent-Based Transmission Chain Simulator

The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. Methods in Ecology and Evolution 11:1002-1007). It is named after the daimones of plague, sickness and disease that escaped Pandora's jar in the Greek mythology. 'nosoi' is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.

Version: 1.1.2
Depends: data.table (≥ 1.12.0), R (≥ 3.5.0)
Imports: stats (≥ 3.5.2), methods (≥ 3.5.2), raster (≥ 2.8-19)
Suggests: testthat (≥ 2.1.0), knitr, rmarkdown, igraph, ggplot2, ggnetwork, intergraph, viridis, gifski, png, gganimate, ape (≥ 5.3), tidytree (≥ 0.3.3), treeio (≥ 1.14.0), ggtree (≥ 2.4.0), magrittr (≥ 1.5), dplyr (≥ 0.8.0), covr
Published: 2024-02-09
DOI: 10.32614/CRAN.package.nosoi
Author: Sebastian Lequime ORCID iD [aut, cre], Paul Bastide ORCID iD [aut], Simon Dellicour ORCID iD [aut], Philippe Lemey ORCID iD [aut], Guy Baele ORCID iD [aut], Thijs Janzen ORCID iD [ctb]
Maintainer: Sebastian Lequime <sebastian.lequime at gmail.com>
BugReports: https://github.com/slequime/nosoi/issues
License: GPL-3
URL: https://github.com/slequime/nosoi, https://slequime.github.io/nosoi/
NeedsCompilation: no
Language: en-US
Citation: nosoi citation info
Materials: NEWS
In views: Epidemiology
CRAN checks: nosoi results

Documentation:

Reference manual: nosoi.pdf
Vignettes: Spread of a pathogen in a continuous space
Spread of a pathogen in a discrete structured population
Spread of a pathogen in a homogeneous population
Getting started
Output and summarization

Downloads:

Package source: nosoi_1.1.2.tar.gz
Windows binaries: r-devel: nosoi_1.1.2.zip, r-release: nosoi_1.1.2.zip, r-oldrel: nosoi_1.1.2.zip
macOS binaries: r-release (arm64): nosoi_1.1.2.tgz, r-oldrel (arm64): nosoi_1.1.2.tgz, r-release (x86_64): nosoi_1.1.2.tgz, r-oldrel (x86_64): nosoi_1.1.2.tgz
Old sources: nosoi archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.